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Zinc in PDB 1ycg: X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase

Protein crystallography data

The structure of X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase, PDB code: 1ycg was solved by R.Silaghi-Dumitrescu, D.M.Kurtz, W.N.Lanzilotta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.71 / 2.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 159.680, 159.680, 278.136, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 24.5

Other elements in 1ycg:

The structure of X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase (pdb code 1ycg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase, PDB code: 1ycg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 1ycg

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Zinc binding site 1 out of 14 in the X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:81.0
occ:1.00
OE2 A:GLU60 2.8 61.0 1.0
CB A:SER2 2.9 68.0 1.0
OG A:SER2 3.0 70.1 1.0
CA A:SER2 3.5 67.0 1.0
CD A:GLU60 3.8 60.8 1.0
N A:SER2 4.1 66.7 1.0
OE1 A:GLU60 4.1 62.1 1.0
C A:SER2 4.8 66.1 1.0

Zinc binding site 2 out of 14 in 1ycg

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Zinc binding site 2 out of 14 in the X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:87.1
occ:1.00
NE2 A:HIS271 2.5 53.5 1.0
OD2 A:ASP275 3.0 54.0 1.0
OD1 A:ASP275 3.1 53.7 1.0
CE1 A:HIS271 3.1 53.4 1.0
CG A:ASP275 3.4 52.2 1.0
CD2 A:HIS271 3.6 51.5 1.0
ND1 A:HIS271 4.3 51.1 1.0
CG A:HIS271 4.6 49.2 1.0
CB A:ASP275 4.8 49.9 1.0

Zinc binding site 3 out of 14 in 1ycg

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Zinc binding site 3 out of 14 in the X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:0.6
occ:1.00
O D:HOH761 1.6 89.9 1.0
OE2 D:GLU388 1.8 60.9 1.0
O A:HOH729 2.2 42.9 1.0
ND1 A:HIS118 2.7 81.8 1.0
CD D:GLU388 2.9 60.2 1.0
CG A:HIS118 3.2 79.7 1.0
CB A:HIS118 3.3 77.3 1.0
OE1 D:GLU388 3.4 60.7 1.0
CE1 A:HIS118 3.6 82.4 1.0
CG D:GLN384 4.0 57.6 1.0
CG D:GLU388 4.1 57.7 1.0
CD2 A:HIS118 4.1 80.4 1.0
O A:HIS118 4.2 76.7 1.0
NE2 D:GLN384 4.3 58.0 1.0
NE2 A:HIS118 4.3 82.0 1.0
CA A:HIS118 4.4 76.1 1.0
C A:HIS118 4.6 75.1 1.0
CD D:GLN384 4.6 60.0 1.0

Zinc binding site 4 out of 14 in 1ycg

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Zinc binding site 4 out of 14 in the X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:1.0
occ:1.00
O A:HOH732 1.4 0.9 1.0
O A:HOH730 1.5 70.3 1.0
O A:HOH731 1.8 67.0 1.0
OE2 A:GLU59 3.1 65.3 1.0
OE2 A:GLU55 3.9 62.5 1.0
CD A:GLU59 4.0 63.9 1.0
O A:PRO56 4.1 48.7 1.0
OE1 A:GLU59 4.3 65.0 1.0
CA A:PRO56 4.4 48.2 1.0
CE A:LYS58 4.5 57.3 1.0
C A:PRO56 4.6 47.9 1.0
OE1 A:GLU55 4.6 63.7 1.0
CD A:GLU55 4.7 62.0 1.0
O A:GLU55 4.8 51.7 1.0

Zinc binding site 5 out of 14 in 1ycg

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Zinc binding site 5 out of 14 in the X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn411

b:92.9
occ:1.00
CB B:SER2 2.9 71.5 1.0
OE2 B:GLU60 3.1 62.9 1.0
OG B:SER2 3.5 75.1 1.0
CA B:SER2 3.6 70.5 1.0
CD B:GLU60 4.0 63.4 1.0
OE1 B:GLU60 4.0 63.8 1.0
N B:SER2 4.1 70.2 1.0
C B:SER2 4.9 69.8 1.0

Zinc binding site 6 out of 14 in 1ycg

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Zinc binding site 6 out of 14 in the X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn412

b:91.6
occ:1.00
NE2 B:HIS271 2.4 59.9 1.0
OD2 B:ASP275 2.8 55.9 1.0
OD1 B:ASP275 3.0 56.4 1.0
CE1 B:HIS271 3.2 60.4 1.0
CG B:ASP275 3.3 55.4 1.0
CD2 B:HIS271 3.5 58.4 1.0
ND1 B:HIS271 4.4 59.7 1.0
CG B:HIS271 4.5 57.9 1.0
CB B:ASP275 4.8 53.2 1.0

Zinc binding site 7 out of 14 in 1ycg

Go back to Zinc Binding Sites List in 1ycg
Zinc binding site 7 out of 14 in the X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn413

b:0.3
occ:1.00
O B:HOH731 1.8 79.9 1.0
O B:HOH733 1.9 67.3 1.0
OD2 B:ASP120 1.9 96.8 1.0
O B:HOH732 1.9 0.1 1.0
O B:HOH734 2.1 61.5 1.0
CG B:ASP120 2.9 95.8 1.0
OD1 B:ASP120 3.2 97.3 1.0
CB B:ASP120 4.3 93.0 1.0

Zinc binding site 8 out of 14 in 1ycg

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Zinc binding site 8 out of 14 in the X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn414

b:0.1
occ:1.00
O B:HOH737 1.6 90.0 1.0
O B:HOH735 2.0 97.0 1.0
O B:HOH736 2.2 78.4 1.0
OE2 B:GLU59 3.4 74.4 1.0
OE2 B:GLU55 3.7 64.2 1.0
O B:PRO56 4.1 49.8 1.0
CA B:PRO56 4.1 51.2 1.0
CD B:GLU59 4.3 71.3 1.0
OE1 B:GLU59 4.3 72.2 1.0
C B:PRO56 4.5 50.6 1.0
CD B:GLU55 4.5 64.5 1.0
OE1 B:GLU55 4.5 66.1 1.0
CE B:LYS58 4.5 58.0 1.0
O B:GLU55 4.6 54.7 1.0
NZ B:LYS58 4.9 59.9 1.0
CB B:PRO56 4.9 50.0 1.0

Zinc binding site 9 out of 14 in 1ycg

Go back to Zinc Binding Sites List in 1ycg
Zinc binding site 9 out of 14 in the X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn421

b:77.0
occ:1.00
OE2 C:GLU60 2.7 52.5 1.0
CB C:SER2 2.9 65.5 1.0
OG C:SER2 3.1 68.9 1.0
CA C:SER2 3.5 62.6 1.0
CD C:GLU60 3.7 51.7 1.0
OE1 C:GLU60 3.9 53.3 1.0
N C:SER2 4.1 62.4 1.0
C C:SER2 4.9 61.1 1.0

Zinc binding site 10 out of 14 in 1ycg

Go back to Zinc Binding Sites List in 1ycg
Zinc binding site 10 out of 14 in the X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn422

b:96.6
occ:1.00
NE2 C:HIS271 2.4 47.6 1.0
OD2 C:ASP275 3.1 56.4 1.0
OD1 C:ASP275 3.2 56.9 1.0
CE1 C:HIS271 3.2 48.0 1.0
CG C:ASP275 3.5 56.5 1.0
CD2 C:HIS271 3.6 46.1 1.0
ND1 C:HIS271 4.4 47.0 1.0
CG C:HIS271 4.6 46.6 1.0

Reference:

R.Silaghi-Dumitrescu, D.M.Kurtz Jr, L.G.Ljungdahl, W.N.Lanzilotta. X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase. Biochemistry V. 44 6492 2005.
ISSN: ISSN 0006-2960
PubMed: 15850383
DOI: 10.1021/BI0473049
Page generated: Wed Oct 16 20:50:24 2024

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